From e9f233fe533e69c578fd8c4c93eee578998cb430 Mon Sep 17 00:00:00 2001
From: Stamatios Sotiropoulos <stam@fmrib.ox.ac.uk>
Date: Wed, 1 Dec 2010 11:41:40 +0000
Subject: [PATCH] added f0 and rician noise options
---
xfibresoptions.h | 110 +++++++++++++++++++++++++----------------------
1 file changed, 59 insertions(+), 51 deletions(-)
diff --git a/xfibresoptions.h b/xfibresoptions.h
index 5ae705d..9a1e71e 100644
--- a/xfibresoptions.h
+++ b/xfibresoptions.h
@@ -1,8 +1,8 @@
-/* BpmOptions.h
+/* xfibresOptions.h
- Mark Woolrich, FMRIB Image Analysis Group
+ Saad Jbabdi, Tim Behrens, Stam Sotiropoulos, FMRIB Image Analysis Group
- Copyright (C) 1999-2000 University of Oxford */
+ Copyright (C) 1999-2010 University of Oxford */
/* CCOPYRIGHT */
@@ -48,6 +48,10 @@ class xfibresOptions {
Option<bool> all_ard;
Option<bool> localinit;
Option<bool> nonlin;
+ Option<bool> rician;
+ Option<bool> f0;
+ Option<bool> ardf0;
+
void parse_command_line(int argc, char** argv, Log& logger);
private:
@@ -69,67 +73,68 @@ class xfibresOptions {
}
inline xfibresOptions::xfibresOptions() :
- verbose(string("-V,--verbose"), false,
- string("switch on diagnostic messages"),
- false, no_argument),
- help(string("-h,--help"), false,
+ verbose(string("-V,--verbose"), false,
+ string("switch on diagnostic messages"),
+ false, no_argument),
+ help(string("-h,--help"), false,
string("display this message"),
false, no_argument),
- logdir(string("--ld,--logdir"), string("logdir"),
- string("log directory (default is logdir)"),
- false, requires_argument),
- forcedir(string("--forcedir"),false,string("Use the actual directory name given - i.e. don't add + to make a new directory"),false,no_argument),
- datafile(string("-k,--data,--datafile"), string("data"),
- string("data file"),
- true, requires_argument),
- maskfile(string("-m,--mask, --maskfile"), string("nodif_brain_mask"),
+ logdir(string("--ld,--logdir"), string("logdir"),
+ string("log directory (default is logdir)"),
+ false, requires_argument),
+ forcedir(string("--forcedir"),false,string("Use the actual directory name given - i.e. don't add + to make a new directory"),false,no_argument),
+ datafile(string("-k,--data,--datafile"), string("data"),
+ string("data file"),
+ true, requires_argument),
+ maskfile(string("-m,--mask, --maskfile"), string("nodif_brain_mask"),
string("mask file"),
true, requires_argument),
- bvecsfile(string("-r,--bvecs"), string("bvecs"),
+ bvecsfile(string("-r,--bvecs"), string("bvecs"),
string("b vectors file"),
true, requires_argument),
- bvalsfile(string("-b,--bvals"), string("bvals"),
+ bvalsfile(string("-b,--bvals"), string("bvals"),
string("b values file"),
true, requires_argument),
- nfibres(string("--nf,--nfibres"),1,
- string("Maximum nukmber of fibres to fit in each voxel (default 1)"),
- false,requires_argument),
- modelnum(string("--model"),1,
- string("Which model to use. 1=mono-exponential (default and required for single shell). 2=continous exponential (for multi-shell experiments)"),
- false,requires_argument),
- fudge(string("--fudge"),1,
+ nfibres(string("--nf,--nfibres"),1,
+ string("Maximum number of fibres to fit in each voxel (default 1)"),
+ false,requires_argument),
+ modelnum(string("--model"),1,
+ string("Which model to use. 1=mono-exponential (default and required for single shell). 2=continous exponential (for multi-shell experiments)"),
+ false,requires_argument),
+ fudge(string("--fudge"),1,
string("ARD fudge factor"),
false,requires_argument),
- njumps(string("--nj,--njumps"),5000,
- string("Num of jumps to be made by MCMC (default is 5000)"),
+ njumps(string("--nj,--njumps"),5000,
+ string("Num of jumps to be made by MCMC (default is 5000)"),
+ false,requires_argument),
+ nburn(string("--bi,--burnin"),0,
+ string("Total num of jumps at start of MCMC to be discarded (default is 0)"),
false,requires_argument),
- nburn(string("--bi,--burnin"),0,
- string("Total num of jumps at start of MCMC to be discarded (default is 0)"),
- false,requires_argument),
- nburn_noard(string("--bn,--burnin_noard"),0,
- string("num of burnin jumps before the ard is imposed (default is 0)"),
+ nburn_noard(string("--bn,--burnin_noard"),0,
+ string("num of burnin jumps before the ard is imposed (default is 0)"),
+ false,requires_argument),
+ sampleevery(string("--se,--sampleevery"),1,
+ string("Num of jumps for each sample (MCMC) (default is 1)"),
+ false,requires_argument),
+ updateproposalevery(string("--upe,--updateproposalevery"),40,
+ string("Num of jumps for each update to the proposal density std (MCMC) (default is 40)"),
+ false,requires_argument),
+ seed(string("--seed"),8665904,string("seed for pseudo random number generator"),
false,requires_argument),
- sampleevery(string("--se,--sampleevery"),1,
- string("Num of jumps for each sample (MCMC) (default is 1)"),
- false,requires_argument),
- updateproposalevery(string("--upe,--updateproposalevery"),40,
- string("Num of jumps for each update to the proposal density std (MCMC) (default is 40)"),
- false,requires_argument),
- seed(string("--seed"),8665904,string("seed for pseudo random number generator"),
- false,requires_argument),
- no_ard(string("--noard"),false,string("Turn ARD off on all fibres"),
- false,no_argument),
- all_ard(string("--allard"),false,string("Turn ARD on on all fibres"),
- false,no_argument),
- localinit(string("--nospat"),false,string("Initialise with tensor, not spatially"),
- false,no_argument),
- nonlin(string("--nonlinear"),false,string("Initialise with nonlinear fitting"),
- false,no_argument),
+ no_ard(string("--noard"),false,string("Turn ARD off on all fibres"),
+ false,no_argument),
+ all_ard(string("--allard"),false,string("Turn ARD on on all fibres"),
+ false,no_argument),
+ localinit(string("--nospat"),false,string("Initialise with tensor, not spatially"),
+ false,no_argument),
+ nonlin(string("--nonlinear"),false,string("Initialise with nonlinear fitting"),
+ false,no_argument),
+ rician(string("--rician"),false,string("Use Rician noise modelling"),false,no_argument),
+ f0(string("--f0"),false,string("Add to the model an unattenuated signal compartment"),false,no_argument),
+ ardf0(string("--ardf0"),false,string("Use ard on f0"),false,no_argument),
options("xfibres v1.11", "xfibres --help (for list of options)\n")
- {
-
-
- try {
+ {
+ try {
options.add(verbose);
options.add(help);
options.add(logdir);
@@ -151,6 +156,9 @@ class xfibresOptions {
options.add(all_ard);
options.add(localinit);
options.add(nonlin);
+ options.add(rician);
+ options.add(f0);
+ options.add(ardf0);
}
catch(X_OptionError& e) {
options.usage();
--
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